Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006667.1 Corchorus capsularis cultivar CVL-1 contig06688, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 43940
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:3752 original size:4 final size:4
Alignment explanation
Indices: 3743--3769 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3733 ATCAGTGATC
3743 TCTG TCTG TCTG TCTG TCTG TCTG TCT
1 TCTG TCTG TCTG TCTG TCTG TCTG TCT
3770 CTCTCTCTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.26, G:0.22, T:0.52
Consensus pattern (4 bp):
TCTG
Found at i:3774 original size:2 final size:2
Alignment explanation
Indices: 3767--3805 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3757 TGTCTGTCTG
3767 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3806 GATTCTGAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:9155 original size:3 final size:3
Alignment explanation
Indices: 9147--9183 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
9137 AAGAGAACCC
9147 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
9184 TGTCTATTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:16872 original size:34 final size:35
Alignment explanation
Indices: 16815--16883 Score: 122
Period size: 34 Copynumber: 2.0 Consensus size: 35
16805 CAACACCAGG
*
16815 GCATTCAATTGATTTTTTTTTAATTGGGTAAATAA
1 GCATTCAATTGATATTTTTTTAATTGGGTAAATAA
16850 GCATTCAATTGA-ATTTTTTTAATTGGGTAAATAA
1 GCATTCAATTGATATTTTTTTAATTGGGTAAATAA
16884 AAGTTTAGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 21 0.64
35 12 0.36
ACGTcount: A:0.33, C:0.06, G:0.14, T:0.46
Consensus pattern (35 bp):
GCATTCAATTGATATTTTTTTAATTGGGTAAATAA
Found at i:18580 original size:12 final size:12
Alignment explanation
Indices: 18563--18595 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
18553 TCGTCACTAA
*
18563 AGTCATCGTCTG
1 AGTCATCATCTG
18575 AGTCATCATCTG
1 AGTCATCATCTG
18587 AGTCATCAT
1 AGTCATCAT
18596 TTGCACGGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.33
Consensus pattern (12 bp):
AGTCATCATCTG
Found at i:27269 original size:17 final size:17
Alignment explanation
Indices: 27236--27269 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
27226 TTGAAGCTTC
*
27236 TTTCTTTTTTTTCTTTT
1 TTTCTTTTTTTGCTTTT
*
27253 TTTCTTTTTTTGGTTTT
1 TTTCTTTTTTTGCTTTT
27270 AAATTTTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.09, G:0.06, T:0.85
Consensus pattern (17 bp):
TTTCTTTTTTTGCTTTT
Found at i:30523 original size:38 final size:37
Alignment explanation
Indices: 30481--30589 Score: 148
Period size: 38 Copynumber: 2.9 Consensus size: 37
30471 CATAAAAGTG
30481 GAATGGACATAAACATTGTATGGAAGACTTATACAGCA
1 GAATGGACATAAACATT-TATGGAAGACTTATACAGCA
* *
30519 GAATGGACATAAACATTT-TGCATAATACTTATACAGCA
1 GAATGGACATAAACATTTATG--GAAGACTTATACAGCA
*
30557 GAATGGACATAAACATTTATGGCAAGAATTATA
1 GAATGGACATAAACATTTATGG-AAGACTTATA
30590 AGGACACACA
Statistics
Matches: 62, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
36 2 0.03
37 1 0.02
38 57 0.92
39 2 0.03
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (37 bp):
GAATGGACATAAACATTTATGGAAGACTTATACAGCA
Found at i:32017 original size:2 final size:2
Alignment explanation
Indices: 32012--32044 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
32002 ACCATGAGCA
32012 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
32045 CACATATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41423 original size:73 final size:73
Alignment explanation
Indices: 41337--41484 Score: 287
Period size: 73 Copynumber: 2.0 Consensus size: 73
41327 GTACAAAAAG
*
41337 AATGAACTTATACGGTATAAAATAAGGACTTATTGTATCAAATTAAGAGTAGATACTTCAAAGAA
1 AATGAACTTATACGGTATAAAATAAGGACTTATTGTATCAAATTAAGAATAGATACTTCAAAGAA
41402 GGAGAATC
66 GGAGAATC
41410 AATGAACTTATACGGTATAAAATAAGGACTTATTGTATCAAATTAAGAATAGATACTTCAAAGAA
1 AATGAACTTATACGGTATAAAATAAGGACTTATTGTATCAAATTAAGAATAGATACTTCAAAGAA
41475 GGAGAATC
66 GGAGAATC
41483 AA
1 AA
41485 AGATTAACTC
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.47, C:0.09, G:0.17, T:0.27
Consensus pattern (73 bp):
AATGAACTTATACGGTATAAAATAAGGACTTATTGTATCAAATTAAGAATAGATACTTCAAAGAA
GGAGAATC
Found at i:42938 original size:19 final size:20
Alignment explanation
Indices: 42911--42948 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
42901 TACTATTATT
42911 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
42931 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
42949 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:43216 original size:24 final size:22
Alignment explanation
Indices: 43117--43246 Score: 86
Period size: 22 Copynumber: 5.8 Consensus size: 22
43107 CTCTATGTGA
* *
43117 TTATCAAAATTTCATAAG-ATGG
1 TTATTAAAATTTCATAGGTA-GG
*
43139 TTATTATAATTTCATGAGG-AGG
1 TTATTAAAATTTCAT-AGGTAGG
* * *
43161 TTATCAAAATTCCATAGTGT-GC
1 TTATTAAAATTTCATAG-GTAGG
**
43183 TTACCAAAATTTCATAGGATCAGG
1 TTATTAAAATTTCATAGG-T-AGG
* * *
43207 TTATTAAAATCTCTTAGGTTGG
1 TTATTAAAATTTCATAGGTAGG
*
43229 TTATTGAAATTTCATAGG
1 TTATTAAAATTTCATAGG
43247 GTGATTAATT
Statistics
Matches: 84, Mismatches: 18, Indels: 12
0.74 0.16 0.11
Matches are distributed among these distances:
21 3 0.04
22 62 0.74
23 4 0.05
24 15 0.18
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (22 bp):
TTATTAAAATTTCATAGGTAGG
Found at i:43294 original size:12 final size:12
Alignment explanation
Indices: 43277--43307 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
43267 TATAGAAAGG
43277 TTATCAAAGAGA
1 TTATCAAAGAGA
*
43289 TTATCAAAGAGG
1 TTATCAAAGAGA
43301 TTATCAA
1 TTATCAA
43308 TGATGTGTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.29
Consensus pattern (12 bp):
TTATCAAAGAGA
Found at i:43344 original size:1 final size:1
Alignment explanation
Indices: 43338--43365 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
43328 AAGGGCCTAG
43338 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
43366 GGTGTATTCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Done.